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  3. Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order h...

    Authors: Yi Shi, Jianjun Zhou, David Arndt, David S Wishart and Guohui Lin
    Citation: BMC Bioinformatics 2008 9:255
    Content type: Research article Published on:

  4. Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactio...

    Authors: Silvana Penco, Massimo Buscema, Maria Cristina Patrosso, Alessandro Marocchi and Enzo Grossi
    Citation: BMC Bioinformatics 2008 9:254
    Content type: Research article Published on:

  5. Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic re...

    Authors: Frank M You, Naxin Huo, Yong Qiang Gu, Ming-cheng Luo, Yaqin Ma, Dave Hane, Gerard R Lazo, Jan Dvorak and Olin D Anderson
    Citation: BMC Bioinformatics 2008 9:253
    Content type: Software Published on:

  6. It is an important pre-processing step to accurately estimate missing values in microarray data, because complete datasets are required in numerous expression profile analysis in bioinformatics. Although sever...

    Authors: Qian Xiang, Xianhua Dai, Yangyang Deng, Caisheng He, Jiang Wang, Jihua Feng and Zhiming Dai
    Citation: BMC Bioinformatics 2008 9:252
    Content type: Research article Published on:

  10. A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only b...

    Authors: Todd H Stokes, JT Torrance, Henry Li and May D Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  11. This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, t...

    Authors: Chang F Quo and May D Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  12. Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular...

    Authors: Lily R Liang, Vinay Mandal, Yi Lu and Deepak Kumar
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  13. Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence al...

    Authors: Guoqing Lu, Shunpu Zhang and Xiang Fang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  14. In DNA microarray gene expression profiling studies, a fundamental task is to extract statistically significant genes that meet certain research hypothesis. Currently, Venn diagram is a frequently used method ...

    Authors: Xutao Deng, Jun Xu and Charles Wang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  15. Tandem mass spectrometry has emerged as a cornerstone of high throughput proteomic studies owing in part to various high throughput search engines which are used to interpret these tandem mass spectra. However...

    Authors: Fang-Xiang Wu, Pierre Gagné, Arnaud Droit and Guy G Poirier
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  16. The traditional (unweighted) k-means is one of the most popular clustering methods for analyzing gene expression data. However, it suffers three major shortcomings. It is sensitive to initial partitions, its r...

    Authors: Fang-Xiang Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  17. In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction of drug interaction on the pathway level is b...

    Authors: Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura and Akihiko Konagaya
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  18. Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of differe...

    Authors: Hiroyuki Mishima, Andrew C Lidral and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  19. Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters t...

    Authors: Mary Qu Yang, James Taylor and Laura Elnitski
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  20. Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray experiments by commonly used ...

    Authors: Xue-Qiang Zeng, Guo-Zheng Li, Jack Y Yang, Mary Qu Yang and Geng-Feng Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  21. Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimen...

    Authors: Guo-Zheng Li, Hao-Hua Meng, Wen-Cong Lu, Jack Y Yang and Mary Qu Yang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  22. Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques...

    Authors: George Chin Jr, Daniel G Chavarria, Grant C Nakamura and Heidi J Sofia
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  23. A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular ...

    Authors: Fei Gu, Hang Chen and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  24. Inference of evolutionary trees using the maximum likelihood principle is NP-hard. Therefore, all practical methods rely on heuristics. The topological transformations often used in heuristics are Nearest Neig...

    Authors: Mao-Zu Guo, Jian-Fu Li and Yang Liu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  25. DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we prop...

    Authors: Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, Yuh-Jyh Hu and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  26. Localization of complex traits by genetic linkage analysis may involve exploration of a vast multidimensional parameter space. The posterior probability of linkage (PPL), a class of statistics for complex trai...

    Authors: Manika Govil, Alberto M Segre and Veronica J Vieland
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  27. The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13–15, 2007. This annual event attracted dozens of bioinformatics professionals and st...

    Authors: Guoqing Lu and Jun Ni
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  28. A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protei...

    Authors: Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom and Baldomero Oliva
    Citation: BMC Bioinformatics 2008 9:249
    Content type: Methodology article Published on:

  31. Association testing is a powerful tool for identifying disease susceptibility genes underlying complex diseases. Technological advances have yielded a dramatic increase in the density of available genetic mark...

    Authors: Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang and Cathy SJ Fann
    Citation: BMC Bioinformatics 2008 9:246
    Content type: Methodology article Published on:

  32. We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kin...

    Authors: Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp and Bostjan Kobe
    Citation: BMC Bioinformatics 2008 9:245
    Content type: Software Published on:

  33. The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by ana...

    Authors: Shameek Biswas, John D Storey and Joshua M Akey
    Citation: BMC Bioinformatics 2008 9:244
    Content type: Methodology article Published on:

  34. Recent advances in global genomic profiling methodologies have enabled multi-dimensional characterization of biological systems. Complete analysis of these genomic profiles require an in depth look at parallel...

    Authors: Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Raymond T Ng, Calum MacAulay and Wan L Lam
    Citation: BMC Bioinformatics 2008 9:243
    Content type: Software Published on:

  35. Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems....

    Authors: W Timothy J White and Michael D Hendy
    Citation: BMC Bioinformatics 2008 9:242
    Content type: Software Published on:

  36. Bioactivity profiling using high-throughput in vitro assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several pu...

    Authors: Richard Judson, Fathi Elloumi, R Woodrow Setzer, Zhen Li and Imran Shah
    Citation: BMC Bioinformatics 2008 9:241
    Content type: Research article Published on:

  37. Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a...

    Authors: Alfredo Braunstein, Roberto Mulet and Andrea Pagnani
    Citation: BMC Bioinformatics 2008 9:240
    Content type: Methodology article Published on:

  38. DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but...

    Authors: Michael C Wendl and Richard K Wilson
    Citation: BMC Bioinformatics 2008 9:239
    Content type: Research article Published on:

  39. Multifactor Dimensionality Reduction (MDR) has been introduced previously as a non-parametric statistical method for detecting gene-gene interactions. MDR performs a dimensional reduction by assigning multi-lo...

    Authors: William S Bush, Todd L Edwards, Scott M Dudek, Brett A McKinney and Marylyn D Ritchie
    Citation: BMC Bioinformatics 2008 9:238
    Content type: Research article Published on:

  40. With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent resul...

    Authors: Leonid Zaslavsky, Yiming Bao and Tatiana A Tatusova
    Citation: BMC Bioinformatics 2008 9:237
    Content type: Methodology article Published on:

  42. Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome com...

    Authors: Jeremy D DeBarry, Renyi Liu and Jeffrey L Bennetzen
    Citation: BMC Bioinformatics 2008 9:235
    Content type: Software Published on:

  45. Utilization of alternative initiation sites for protein translation directed by non-AUG codons in mammalian mRNAs is observed with increasing frequency. Alternative initiation sites are utilized for the synthe...

    Authors: Jill L Wegrzyn, Thomas M Drudge, Faramarz Valafar and Vivian Hook
    Citation: BMC Bioinformatics 2008 9:232
    Content type: Research article Published on:

  48. The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are invol...

    Authors: Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo López and Toby J Gibson
    Citation: BMC Bioinformatics 2008 9:229
    Content type: Methodology article Published on:

  49. Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admitt...

    Authors: Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu and Anne Siegel
    Citation: BMC Bioinformatics 2008 9:228
    Content type: Methodology article Published on:

  50. Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emp...

    Authors: Anatolij P Potapov, Björn Goemann and Edgar Wingender
    Citation: BMC Bioinformatics 2008 9:227
    Content type: Methodology article Published on:

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